genotypeToCharacter {GWASTools} | R Documentation

## Convert number of A alleles to character genotypes

### Description

Converts a vector or matrix of genotypes encoded as number of A alleles to character strings of the form "A/B".

### Usage

    genotypeToCharacter(geno, alleleA=NULL, alleleB=NULL, sort=TRUE)

### Arguments

`geno` | Vector or matrix of genotype values, encoded as number of A alleles. If a matrix, dimensions should be (snp, sample).
`alleleA` | Character vector with allele A.
`alleleB` | Character vector with allele B.
`sort` | Logical for whether to sort alleles lexographically ("G/T" instead of "T/G").

### Details

If `geno` is a vector, `alleleA` and `alleleB` should have the same length as `geno` or length 1 (in the latter case the values are recycled).

If `geno` is a matrix, length of `alleleA` and `alleleB` should be equal to the number of rows of `geno`.

If `alelleA` or `alleleB` is `NULL`, returned genotypes will have values "A/A", "A/B", or "B/B".

### Value

Character vector or matrix of the same dimensions as `geno`.

### Author(s)

Stephanie Gogarten

### See Also

`GenotypeData`

### Examples

    geno <- matrix(c(0,1,2,0,1,2,1,NA), nrow=4)
    alleleA <- c("A","T","C","T")
    alleleB <- c("C","G","G","A")
    genotypeToCharacter(geno, alleleA, alleleB)

[Package GWASTools version 1.26.1 Index]